Tracking Git commits

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Core commits
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Recent Commits to bioperl-live:master

add latest changes to, um, Changes
Add for test
Add tests for bug #88, spliced_seq()
Eric Snyder's bug fix for spliced_seq() error on reverse strand
one more for changes
database name changed
have to ignore possibly bad cert to get this working, and tests were inconsistent
have to ignore possibly bad cert to get this working
have to ignore possibly bad cert to get this working
yep, another flappy test
another flappy test
squash waffling test
minor cleanup
ad more updates
remove debugging
document minor changes
bump version; this seems to be caught by latest M::B and may have been ignored due to subclassing
Merge branch 'master' of github.com:bioperl/bioperl-live
no_index means 'do not index any modules nor add them to provides in META', which means these get skipped in META.json/yml; if we don't want these, we add them to MANIFEST.SKIP, the whole purpose of that file
Merge pull request #85 from nyamned/patch-1
Run commits
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Recent Commits to bioperl-run:master

WBCommandExts.t: Fixed a pending TODO related to
Update Build.PL, MYMETA.json with build dependencies
no dependencies on any of the Test::* or Sub::Uplevel in any test (except maybe through Bio::Root::Test; in any case should not be frozen in the distro, but tests that break due to updates should instead be updated themselves.
Update Build.PL with config_requires and build_requires; add MANIFEST
Merge branch 'master' into topic/move_WrapperBase
fixed translate_params tests according to discussion at commit a6d0dc2; removed TODO around translate_params test
move StandAloneBlast* and WrapperBase* from root/Bio... to root/lib/Bio...
Merge branch 'master' of ../move_WrapperBase/bioperl-wb into topic/move_WrapperBase
test parameters independent of their order as issued on command line
Removed empty file Bio/Tools/Run/hmmer3.pm, which seems
Merge branch 'master' of https://github.com/bioperl/bioperl-live
giving new meaning to the term "git", moving Est2Genome.pm back where it belongs
adding back Est2Genome.pm -DOH
loosened validation for outfmt in BlastMethods to allow quoted multiple values (new blast+ feature); added tests for issue 12 to SABlastPlus.t
fix parsing edge case
issue 12: changes to _translate_params that allow quoted option values
POD updates
Really die if EMBOSS is not found
Merge branch 'master' of github.com:bioperl/bioperl-live
Merge pull request #71 from nathanweeks/issue/bio-seqfeature-lite-strand
Ext commits
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Recent Commits to bioperl-ext:master

markdown-ize README
moved Bio::Tools::HMM and Bio::Ext::HMM into their own distro, got them compiling cleanly. tests not passing yet
use UPPPER_TOL to catch the case when the expectation maximization step
fixed Vitebi typo
Fixed the typemap and also a memory bug in viterbi function in HMM.xs
adding FEEDBACK:Support section to pod
Bump to 1.007 (similar to trunk)
ext patches (courtesy Thomas Jahns)
get rid of some unended comment warnings from C compiler
-fPIC needed for lib construction
include errno definition
removed DEBUG=1
IUPAC DNA support
IUPAC DNA test case
Add some helper code and tests to demo evalue oddities (bug 1857); casting issue?
Add cast to correct pointer type (get rid of warnings)
update version to last bioperl release
bug 2329
bug 2074/2329
Removed Aaron's old test script (now in t/staden_read.t). Do we modify master ext makefile to account for this?
Bioperl-DB (BioSQL)
RSS

Recent Commits to bioperl-db:master

Minor POD edits and reformatting
Add some useful example code
updates since last release
update skipped files
add MANIFEST.SKIP
buzgilla -> redmine
[RT 44466] remove corba-related scripts, now obsolete
squash perl 5.12 warning
ignore conf file
add minimal .gitignore file
weird duplication removed
committing patch for bug #2958
test commit to check SVN::Notify
Build.PL now checks for DBD drivers and attempts to DTRT
remove MANIFEST.SKIP
update Changes
fix empty POD section
some pod cleaning
main trunk version is wrong
* 02species.t now compared to similarly behaving instance, also creates comparable array
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